[med-svn] [python-cutadapt] 03/03: first packaging setup
Olivier Sallou
osallou at debian.org
Mon Aug 17 08:29:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch feature_packaging
in repository python-cutadapt.
commit ffd228cff37e7cab6f1580928af826a39fb722f0
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Mon Aug 17 09:25:36 2015 +0200
first packaging setup
---
debian/README.Debian | 8 +-
debian/README.source | 10 --
debian/changelog | 2 +-
debian/control | 53 +++++--
debian/copyright | 33 ++--
debian/cutadapt.man1 | 307 +++++++++++++++++++++++++++++++++++++
debian/cutadapt3.man1 | 307 +++++++++++++++++++++++++++++++++++++
debian/docs | 0
debian/init.d.ex | 166 --------------------
debian/manpage.1.ex | 56 -------
debian/manpage.sgml.ex | 154 -------------------
debian/manpage.xml.ex | 291 -----------------------------------
debian/menu.ex | 2 -
debian/postinst.ex | 39 -----
debian/postrm.ex | 37 -----
debian/preinst.ex | 35 -----
debian/prerm.ex | 38 -----
debian/python-cutadapt.cron.d.ex | 4 -
debian/python-cutadapt.default.ex | 10 --
debian/python-cutadapt.doc-base.EX | 20 ---
debian/python-cutadapt.manpages | 1 +
debian/python3-cutadapt.manpages | 1 +
debian/rules | 12 +-
debian/watch | 3 +
debian/watch.ex | 23 ---
25 files changed, 690 insertions(+), 922 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
index e8ba74f..74c0bc3 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -1,6 +1,2 @@
-python-cutadapt for Debian
---------------------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 09:09:04 +0200
+Binary has been renamed cutadapt3 for Python 3.
+For Python 2.x, original cutadapt name has been kept.
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index d463a61..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,10 +0,0 @@
-python-cutadapt for Debian
---------------------------
-
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
-
-
-
- -- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 09:09:04 +0200
-
diff --git a/debian/changelog b/debian/changelog
index c1ce06e..5aceb66 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
python-cutadapt (1.8.3-1) unstable; urgency=low
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #nnnn)
-- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 09:09:04 +0200
diff --git a/debian/control b/debian/control
index d0417ff..61c5ccc 100644
--- a/debian/control
+++ b/debian/control
@@ -1,15 +1,48 @@
Source: python-cutadapt
-Section: unknown
+Section: python
Priority: optional
-Maintainer: Olivier Sallou <osallou at debian.org>
-Build-Depends: debhelper (>= 9)
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all,
+ python-all-dev,
+ python-setuptools,
+ cython,
+ python3-all,
+ python3-all-dev,
+ python3-setuptools,
+ python3-six,
+ cython3
+X-Python-Version: >= 2.7
+X-Python3-Version: >= 3.4
Standards-Version: 3.9.6
-Homepage: <insert the upstream URL, if relevant>
-#Vcs-Git: git://anonscm.debian.org/collab-maint/python-cutadapt.git
-#Vcs-Browser: https://anonscm.debian.org/gitweb/?p=collab-maint/python-cutadapt.git;a=summary
+Homepage: http://pypi.python.org/pypi/cutadapt
+Vcs-Git: git://anonscm.debian.org/debian-med/python-cutadapt.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-cutadapt.git
Package: python-cutadapt
-Architecture: all
-Depends: ${misc:Depends}
-Description: <insert up to 60 chars description>
- <insert long description, indented with spaces>
+Architecture: any
+Depends: ${misc:Depends},${python:Depends},${shlibs:Depends}
+Description: Clean biological sequences from high-throughput sequencing reads
+ Cutadapt helps with biological sequence clean tasks by finding the adapter
+ or primer sequences in an error-tolerant way.
+ It can also modify and filter reads in various ways.
+ Adapter sequences can contain IUPAC wildcard characters.
+ Also, paired-end reads and even colorspace data is supported.
+ If you want, you can also just demultiplex your input data, without removing
+ adapter sequences at all.
+
+
+Package: python3-cutadapt
+Architecture: any
+Depends: ${misc:Depends},${python3:Depends},${shlibs:Depends}
+Description: Clean biological sequences from high-throughput sequencing reads
+ Cutadapt helps with biological sequence clean tasks by finding the adapter
+ or primer sequences in an error-tolerant way.
+ It can also modify and filter reads in various ways.
+ Adapter sequences can contain IUPAC wildcard characters.
+ Also, paired-end reads and even colorspace data is supported.
+ If you want, you can also just demultiplex your input data, without removing
+ adapter sequences at all.
+
diff --git a/debian/copyright b/debian/copyright
index 67b4320..cc2bf20 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,18 +1,28 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: python-cutadapt
-Source: <url://example.com>
+Source: http://pypi.python.org/pypi/cutadapt
Files: *
-Copyright: <years> <put author's name and email here>
- <years> <likewise for another author>
-License: <special license>
- <Put the license of the package here indented by 1 space>
- <This follows the format of Description: lines in control file>
+Copyright: 2010-2015 Marcel Martin <marcel.martin at scilifelab.se>
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
.
- <Including paragraphs>
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
-# If you want to use GPL v2 or later for the /debian/* files use
-# the following clauses, or change it to suit. Delete these two lines
Files: debian/*
Copyright: 2015 Olivier Sallou <osallou at debian.org>
License: GPL-2+
@@ -31,8 +41,3 @@ License: GPL-2+
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
-# Please avoid picking licenses with terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/cutadapt.man1 b/debian/cutadapt.man1
new file mode 100644
index 0000000..4a2023b
--- /dev/null
+++ b/debian/cutadapt.man1
@@ -0,0 +1,307 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH CUTADAPT "1" "August 2015" "cutadapt 1.8.3" "User Commands"
+.SH NAME
+cutadapt \- manual page for cutadapt 1.8.3
+.SH DESCRIPTION
+cutadapt version 1.8.3
+Copyright \(co 2010\-2015 Marcel Martin <marcel.martin at scilifelab.se>
+.PP
+cutadapt removes adapter sequences from high\-throughput sequencing reads.
+.SS "Usage:"
+.IP
+cutadapt \fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
+.SS "For paired-end reads:"
+.IP
+cutadapt \fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
+.PP
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. The reverse complement is *not* automatically
+searched. All reads from input.fastq will be written to output.fastq with the
+adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
+sequences can be given (use further \fB\-a\fR options), but only the best\-matching
+adapter will be removed.
+.PP
+Input may also be in FASTA format. Compressed input and output is supported and
+auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
+standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
+.SS "Some other available features are:"
+.IP
+* Various other adapter types (5' adapters, "mixed" 5'/3' adapters etc.)
+* Trimming a fixed number of bases
+* Quality trimming
+* Trimming colorspace reads
+* Filtering reads by various criteria
+.PP
+Use "cutadapt \fB\-\-help\fR" to see all command\-line options.
+See http://cutadapt.readthedocs.org/ for full documentation.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
+Input file format; can be either 'fasta', 'fastq' or
+\&'sra\-fastq'. Ignored when reading csfasta/qual files
+(default: auto\-detect from file name extension).
+.IP
+Options that influence how the adapters are found:
+.IP
+Each of the following three parameters (\fB\-a\fR, \fB\-b\fR, \fB\-g\fR) can be used
+multiple times and in any combination to search for an entire set of
+adapters of possibly different types. Only the best matching adapter
+is trimmed from each read (but see the \fB\-\-times\fR option). Instead of
+giving an adapter directly, you can also write file:FILE and the
+adapter sequences will be read from the given FILE (which must be in
+FASTA format).
+.TP
+\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 3' end.
+The adapter itself and anything that follows is
+trimmed. If the adapter sequence ends with the '$'
+character, the adapter is anchored to the end of the
+read and only found if it is a suffix of the read.
+.TP
+\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 5' end.
+If the adapter sequence starts with the character '^',
+the adapter is 'anchored'. An anchored adapter must
+appear in its entirety at the 5' end of the read (it
+is a prefix of the read). A non\-anchored adapter may
+appear partially at the 5' end, or it may occur within
+the read. If it is found within a read, the sequence
+preceding the adapter is also trimmed. In all cases,
+the adapter itself is trimmed.
+.TP
+\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 5' or
+3' end. If the adapter is found within the read or
+overlapping the 3' end of the read, the behavior is
+the same as for the \fB\-a\fR option. If the adapter overlaps
+the 5' end (beginning of the read), the initial
+portion of the read matching the adapter is trimmed,
+but anything that follows is kept.
+.TP
+\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
+Maximum allowed error rate (no. of errors divided by
+the length of the matching region) (default: 0.1)
+.TP
+\fB\-\-no\-indels\fR
+Do not allow indels in the alignments (allow only
+mismatches). Currently only supported for anchored
+adapters. (default: allow both mismatches and indels)
+.TP
+\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
+Try to remove adapters at most COUNT times. Useful
+when an adapter gets appended multiple times (default:
+1).
+.TP
+\fB\-O\fR LENGTH, \fB\-\-overlap\fR=\fI\,LENGTH\/\fR
+Minimum overlap length. If the overlap between the
+read and the adapter is shorter than LENGTH, the read
+is not modified. This reduces the no. of bases trimmed
+purely due to short random adapter matches (default:
+3).
+.TP
+\fB\-\-match\-read\-wildcards\fR
+Allow IUPAC wildcards in reads (default: False).
+.TP
+\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
+Do not interpret IUPAC wildcards in adapters.
+.IP
+Options for filtering of processed reads:
+.TP
+\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
+Discard reads that contain the adapter instead of
+trimming them. Also use \fB\-O\fR in order to avoid throwing
+away too many randomly matching reads!
+.TP
+\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
+Discard reads that do not contain the adapter.
+.TP
+\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are shorter than LENGTH.
+Reads that are too short even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted (default: 0).
+.TP
+\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are longer than LENGTH.
+Reads that are too long even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted (default: no limit).
+.TP
+\fB\-\-no\-trim\fR
+Match and redirect reads to output/untrimmed\-output as
+usual, but do not remove adapters.
+.TP
+\fB\-\-max\-n\fR=\fI\,LENGTH\/\fR
+The max proportion of N's allowed in a read. A number
+< 1 will be treated as a proportion while a number > 1
+will be treated as the maximum number of N's
+contained.
+.TP
+\fB\-\-mask\-adapter\fR
+Mask adapters with 'N' characters instead of trimming
+them.
+.IP
+Options that influence what gets output to where:
+.TP
+\fB\-\-quiet\fR
+Do not print a report at the end.
+.TP
+\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
+Write modified reads to FILE. FASTQ or FASTA format is
+chosen depending on input. The summary report is sent
+to standard output. Use '{name}' in FILE to
+demultiplex reads into multiple files. (default:
+trimmed reads are written to standard output)
+.TP
+\fB\-\-info\-file\fR=\fI\,FILE\/\fR
+Write information about each read and its adapter
+matches into FILE. See the documentation for the file
+format.
+.TP
+\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
+When the adapter matches in the middle of a read,
+write the rest (after the adapter) into FILE.
+.TP
+\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
+When the adapter has wildcard bases ('N's), write
+adapter bases matching wildcard positions to FILE.
+When there are indels in the alignment, this will
+often not be accurate.
+.TP
+\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
+Write reads that are too short (according to length
+specified by \fB\-m\fR) to FILE. (default: discard reads)
+.TP
+\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
+Write reads that are too long (according to length
+specified by \fB\-M\fR) to FILE. (default: discard reads)
+.TP
+\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
+Write reads that do not contain the adapter to FILE.
+(default: output to same file as trimmed reads)
+.IP
+Additional modifications to the reads:
+.TP
+\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
+Remove LENGTH bases from the beginning or end of each
+read. If LENGTH is positive, the bases are removed
+from the beginning of each read. If LENGTH is
+negative, the bases are removed from the end of each
+read. This option can be specified twice if the
+LENGTHs have different signs.
+.TP
+\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
+Trim low\-quality bases from 5' and/or 3' ends of reads
+before adapter removal. If one value is given, only
+the 3' end is trimmed. If two comma\-separated cutoffs
+are given, the 5' end is trimmed with the first
+cutoff, the 3' end with the second. The algorithm is
+the same as the one used by BWA (see documentation).
+(default: no trimming)
+.TP
+\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
+Assume that quality values are encoded as
+ascii(quality + QUALITY_BASE). The default (33) is
+usually correct, except for reads produced by some
+versions of the Illumina pipeline, where this should
+be set to 64. (Default: 33)
+.TP
+\fB\-\-trim\-n\fR
+Trim N's on ends of reads.
+.TP
+\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
+Add this prefix to read names
+.TP
+\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
+Add this suffix to read names
+.TP
+\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
+Remove this suffix from read names if present. Can be
+given multiple times.
+.TP
+\fB\-c\fR, \fB\-\-colorspace\fR
+Colorspace mode: Also trim the color that is adjacent
+to the found adapter.
+.TP
+\fB\-d\fR, \fB\-\-double\-encode\fR
+When in colorspace, double\-encode colors (map
+0,1,2,3,4 to A,C,G,T,N).
+.TP
+\fB\-t\fR, \fB\-\-trim\-primer\fR
+When in colorspace, trim primer base and the first
+color (which is the transition to the first
+nucleotide)
+.TP
+\fB\-\-strip\-f3\fR
+For colorspace: Strip the _F3 suffix of read names
+.TP
+\fB\-\-maq\fR, \fB\-\-bwa\fR
+MAQ\- and BWA\-compatible colorspace output. This
+enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
+.TP
+\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
+Search for TAG followed by a decimal number in the
+description field of the read. Replace the decimal
+number with the correct length of the trimmed read.
+For example, use \fB\-\-length\-tag\fR 'length=' to correct
+fields like 'length=123'.
+.TP
+\fB\-\-no\-zero\-cap\fR
+Do not change negative quality values to zero.
+Colorspace quality values of \fB\-1\fR would appear as spaces
+in the output FASTQ file. Since many tools have
+problems with that, negative qualities are converted
+to zero when trimming colorspace data. Use this option
+to keep negative qualities.
+.TP
+\fB\-z\fR, \fB\-\-zero\-cap\fR
+Change negative quality values to zero. This is
+enabled by default when \fB\-c\fR/\-\-colorspace is also
+enabled. Use the above option to disable it.
+.IP
+Paired\-end options.:
+.IP
+The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts.
+.TP
+\fB\-A\fR ADAPTER
+3' adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-G\fR ADAPTER
+5' adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-B\fR ADAPTER
+5'/3 adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-U\fR LENGTH
+Remove LENGTH bases from the beginning or end of each
+read (see \fB\-\-cut\fR).
+.TP
+\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to FILE.
+.TP
+\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
+Write the second read in a pair to this FILE when no
+adapter was found in the first read. Use this option
+together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. (Default: output to same file as trimmed
+reads.)
+.SH "SEE ALSO"
+The full documentation for
+.B cutadapt
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B cutadapt
+programs are properly installed at your site, the command
+.IP
+.B info cutadapt
+.PP
+should give you access to the complete manual.
diff --git a/debian/cutadapt3.man1 b/debian/cutadapt3.man1
new file mode 100644
index 0000000..4a2023b
--- /dev/null
+++ b/debian/cutadapt3.man1
@@ -0,0 +1,307 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH CUTADAPT "1" "August 2015" "cutadapt 1.8.3" "User Commands"
+.SH NAME
+cutadapt \- manual page for cutadapt 1.8.3
+.SH DESCRIPTION
+cutadapt version 1.8.3
+Copyright \(co 2010\-2015 Marcel Martin <marcel.martin at scilifelab.se>
+.PP
+cutadapt removes adapter sequences from high\-throughput sequencing reads.
+.SS "Usage:"
+.IP
+cutadapt \fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
+.SS "For paired-end reads:"
+.IP
+cutadapt \fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
+.PP
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. The reverse complement is *not* automatically
+searched. All reads from input.fastq will be written to output.fastq with the
+adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
+sequences can be given (use further \fB\-a\fR options), but only the best\-matching
+adapter will be removed.
+.PP
+Input may also be in FASTA format. Compressed input and output is supported and
+auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
+standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
+.SS "Some other available features are:"
+.IP
+* Various other adapter types (5' adapters, "mixed" 5'/3' adapters etc.)
+* Trimming a fixed number of bases
+* Quality trimming
+* Trimming colorspace reads
+* Filtering reads by various criteria
+.PP
+Use "cutadapt \fB\-\-help\fR" to see all command\-line options.
+See http://cutadapt.readthedocs.org/ for full documentation.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
+Input file format; can be either 'fasta', 'fastq' or
+\&'sra\-fastq'. Ignored when reading csfasta/qual files
+(default: auto\-detect from file name extension).
+.IP
+Options that influence how the adapters are found:
+.IP
+Each of the following three parameters (\fB\-a\fR, \fB\-b\fR, \fB\-g\fR) can be used
+multiple times and in any combination to search for an entire set of
+adapters of possibly different types. Only the best matching adapter
+is trimmed from each read (but see the \fB\-\-times\fR option). Instead of
+giving an adapter directly, you can also write file:FILE and the
+adapter sequences will be read from the given FILE (which must be in
+FASTA format).
+.TP
+\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 3' end.
+The adapter itself and anything that follows is
+trimmed. If the adapter sequence ends with the '$'
+character, the adapter is anchored to the end of the
+read and only found if it is a suffix of the read.
+.TP
+\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 5' end.
+If the adapter sequence starts with the character '^',
+the adapter is 'anchored'. An anchored adapter must
+appear in its entirety at the 5' end of the read (it
+is a prefix of the read). A non\-anchored adapter may
+appear partially at the 5' end, or it may occur within
+the read. If it is found within a read, the sequence
+preceding the adapter is also trimmed. In all cases,
+the adapter itself is trimmed.
+.TP
+\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that was ligated to the 5' or
+3' end. If the adapter is found within the read or
+overlapping the 3' end of the read, the behavior is
+the same as for the \fB\-a\fR option. If the adapter overlaps
+the 5' end (beginning of the read), the initial
+portion of the read matching the adapter is trimmed,
+but anything that follows is kept.
+.TP
+\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
+Maximum allowed error rate (no. of errors divided by
+the length of the matching region) (default: 0.1)
+.TP
+\fB\-\-no\-indels\fR
+Do not allow indels in the alignments (allow only
+mismatches). Currently only supported for anchored
+adapters. (default: allow both mismatches and indels)
+.TP
+\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
+Try to remove adapters at most COUNT times. Useful
+when an adapter gets appended multiple times (default:
+1).
+.TP
+\fB\-O\fR LENGTH, \fB\-\-overlap\fR=\fI\,LENGTH\/\fR
+Minimum overlap length. If the overlap between the
+read and the adapter is shorter than LENGTH, the read
+is not modified. This reduces the no. of bases trimmed
+purely due to short random adapter matches (default:
+3).
+.TP
+\fB\-\-match\-read\-wildcards\fR
+Allow IUPAC wildcards in reads (default: False).
+.TP
+\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
+Do not interpret IUPAC wildcards in adapters.
+.IP
+Options for filtering of processed reads:
+.TP
+\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
+Discard reads that contain the adapter instead of
+trimming them. Also use \fB\-O\fR in order to avoid throwing
+away too many randomly matching reads!
+.TP
+\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
+Discard reads that do not contain the adapter.
+.TP
+\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are shorter than LENGTH.
+Reads that are too short even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted (default: 0).
+.TP
+\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are longer than LENGTH.
+Reads that are too long even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted (default: no limit).
+.TP
+\fB\-\-no\-trim\fR
+Match and redirect reads to output/untrimmed\-output as
+usual, but do not remove adapters.
+.TP
+\fB\-\-max\-n\fR=\fI\,LENGTH\/\fR
+The max proportion of N's allowed in a read. A number
+< 1 will be treated as a proportion while a number > 1
+will be treated as the maximum number of N's
+contained.
+.TP
+\fB\-\-mask\-adapter\fR
+Mask adapters with 'N' characters instead of trimming
+them.
+.IP
+Options that influence what gets output to where:
+.TP
+\fB\-\-quiet\fR
+Do not print a report at the end.
+.TP
+\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
+Write modified reads to FILE. FASTQ or FASTA format is
+chosen depending on input. The summary report is sent
+to standard output. Use '{name}' in FILE to
+demultiplex reads into multiple files. (default:
+trimmed reads are written to standard output)
+.TP
+\fB\-\-info\-file\fR=\fI\,FILE\/\fR
+Write information about each read and its adapter
+matches into FILE. See the documentation for the file
+format.
+.TP
+\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
+When the adapter matches in the middle of a read,
+write the rest (after the adapter) into FILE.
+.TP
+\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
+When the adapter has wildcard bases ('N's), write
+adapter bases matching wildcard positions to FILE.
+When there are indels in the alignment, this will
+often not be accurate.
+.TP
+\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
+Write reads that are too short (according to length
+specified by \fB\-m\fR) to FILE. (default: discard reads)
+.TP
+\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
+Write reads that are too long (according to length
+specified by \fB\-M\fR) to FILE. (default: discard reads)
+.TP
+\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
+Write reads that do not contain the adapter to FILE.
+(default: output to same file as trimmed reads)
+.IP
+Additional modifications to the reads:
+.TP
+\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
+Remove LENGTH bases from the beginning or end of each
+read. If LENGTH is positive, the bases are removed
+from the beginning of each read. If LENGTH is
+negative, the bases are removed from the end of each
+read. This option can be specified twice if the
+LENGTHs have different signs.
+.TP
+\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
+Trim low\-quality bases from 5' and/or 3' ends of reads
+before adapter removal. If one value is given, only
+the 3' end is trimmed. If two comma\-separated cutoffs
+are given, the 5' end is trimmed with the first
+cutoff, the 3' end with the second. The algorithm is
+the same as the one used by BWA (see documentation).
+(default: no trimming)
+.TP
+\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
+Assume that quality values are encoded as
+ascii(quality + QUALITY_BASE). The default (33) is
+usually correct, except for reads produced by some
+versions of the Illumina pipeline, where this should
+be set to 64. (Default: 33)
+.TP
+\fB\-\-trim\-n\fR
+Trim N's on ends of reads.
+.TP
+\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
+Add this prefix to read names
+.TP
+\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
+Add this suffix to read names
+.TP
+\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
+Remove this suffix from read names if present. Can be
+given multiple times.
+.TP
+\fB\-c\fR, \fB\-\-colorspace\fR
+Colorspace mode: Also trim the color that is adjacent
+to the found adapter.
+.TP
+\fB\-d\fR, \fB\-\-double\-encode\fR
+When in colorspace, double\-encode colors (map
+0,1,2,3,4 to A,C,G,T,N).
+.TP
+\fB\-t\fR, \fB\-\-trim\-primer\fR
+When in colorspace, trim primer base and the first
+color (which is the transition to the first
+nucleotide)
+.TP
+\fB\-\-strip\-f3\fR
+For colorspace: Strip the _F3 suffix of read names
+.TP
+\fB\-\-maq\fR, \fB\-\-bwa\fR
+MAQ\- and BWA\-compatible colorspace output. This
+enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
+.TP
+\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
+Search for TAG followed by a decimal number in the
+description field of the read. Replace the decimal
+number with the correct length of the trimmed read.
+For example, use \fB\-\-length\-tag\fR 'length=' to correct
+fields like 'length=123'.
+.TP
+\fB\-\-no\-zero\-cap\fR
+Do not change negative quality values to zero.
+Colorspace quality values of \fB\-1\fR would appear as spaces
+in the output FASTQ file. Since many tools have
+problems with that, negative qualities are converted
+to zero when trimming colorspace data. Use this option
+to keep negative qualities.
+.TP
+\fB\-z\fR, \fB\-\-zero\-cap\fR
+Change negative quality values to zero. This is
+enabled by default when \fB\-c\fR/\-\-colorspace is also
+enabled. Use the above option to disable it.
+.IP
+Paired\-end options.:
+.IP
+The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts.
+.TP
+\fB\-A\fR ADAPTER
+3' adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-G\fR ADAPTER
+5' adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-B\fR ADAPTER
+5'/3 adapter to be removed from the second read in a
+pair.
+.TP
+\fB\-U\fR LENGTH
+Remove LENGTH bases from the beginning or end of each
+read (see \fB\-\-cut\fR).
+.TP
+\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to FILE.
+.TP
+\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
+Write the second read in a pair to this FILE when no
+adapter was found in the first read. Use this option
+together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. (Default: output to same file as trimmed
+reads.)
+.SH "SEE ALSO"
+The full documentation for
+.B cutadapt
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B cutadapt
+programs are properly installed at your site, the command
+.IP
+.B info cutadapt
+.PP
+should give you access to the complete manual.
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index e69de29..0000000
diff --git a/debian/init.d.ex b/debian/init.d.ex
deleted file mode 100644
index 9b9b3d6..0000000
--- a/debian/init.d.ex
+++ /dev/null
@@ -1,166 +0,0 @@
-#!/bin/sh
-### BEGIN INIT INFO
-# Provides: python-cutadapt
-# Required-Start: $local_fs $network $remote_fs $syslog
-# Required-Stop: $local_fs $network $remote_fs $syslog
-# Default-Start: 2 3 4 5
-# Default-Stop: 0 1 6
-# Short-Description: <Enter a short description of the software>
-# Description: <Enter a long description of the software>
-# <...>
-# <...>
-### END INIT INFO
-
-# Author: Olivier Sallou <osallou at debian.org>
-
-# Do NOT "set -e"
-
-# PATH should only include /usr/* if it runs after the mountnfs.sh script
-PATH=/sbin:/usr/sbin:/bin:/usr/bin
-DESC="python-cutadapt"
-NAME=python-cutadapt
-DAEMON=/usr/sbin/python-cutadapt
-DAEMON_ARGS=""
-PIDFILE=/var/run/$NAME.pid
-SCRIPTNAME=/etc/init.d/$NAME
-
-# Exit if the package is not installed
-[ -x "$DAEMON" ] || exit 0
-
-# Read configuration variable file if it is present
-[ -r /etc/default/$NAME ] && . /etc/default/$NAME
-
-# Load the VERBOSE setting and other rcS variables
-. /lib/init/vars.sh
-
-# Define LSB log_* functions.
-# Depend on lsb-base (>= 3.2-14) to ensure that this file is present
-# and status_of_proc is working.
-. /lib/lsb/init-functions
-
-#
-# Function that starts the daemon/service
-#
-do_start()
-{
- # Return
- # 0 if daemon has been started
- # 1 if daemon was already running
- # 2 if daemon could not be started
- start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON --test > /dev/null \
- || return 1
- start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON -- \
- $DAEMON_ARGS \
- || return 2
- # The above code will not work for interpreted scripts, use the next
- # six lines below instead (Ref: #643337, start-stop-daemon(8) )
- #start-stop-daemon --start --quiet --pidfile $PIDFILE --startas $DAEMON \
- # --name $NAME --test > /dev/null \
- # || return 1
- #start-stop-daemon --start --quiet --pidfile $PIDFILE --startas $DAEMON \
- # --name $NAME -- $DAEMON_ARGS \
- # || return 2
-
- # Add code here, if necessary, that waits for the process to be ready
- # to handle requests from services started subsequently which depend
- # on this one. As a last resort, sleep for some time.
-}
-
-#
-# Function that stops the daemon/service
-#
-do_stop()
-{
- # Return
- # 0 if daemon has been stopped
- # 1 if daemon was already stopped
- # 2 if daemon could not be stopped
- # other if a failure occurred
- start-stop-daemon --stop --quiet --retry=TERM/30/KILL/5 --pidfile $PIDFILE --name $NAME
- RETVAL="$?"
- [ "$RETVAL" = 2 ] && return 2
- # Wait for children to finish too if this is a daemon that forks
- # and if the daemon is only ever run from this initscript.
- # If the above conditions are not satisfied then add some other code
- # that waits for the process to drop all resources that could be
- # needed by services started subsequently. A last resort is to
- # sleep for some time.
- start-stop-daemon --stop --quiet --oknodo --retry=0/30/KILL/5 --exec $DAEMON
- [ "$?" = 2 ] && return 2
- # Many daemons don't delete their pidfiles when they exit.
- rm -f $PIDFILE
- return "$RETVAL"
-}
-
-#
-# Function that sends a SIGHUP to the daemon/service
-#
-do_reload() {
- #
- # If the daemon can reload its configuration without
- # restarting (for example, when it is sent a SIGHUP),
- # then implement that here.
- #
- start-stop-daemon --stop --signal 1 --quiet --pidfile $PIDFILE --name $NAME
- return 0
-}
-
-case "$1" in
- start)
- [ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC" "$NAME"
- do_start
- case "$?" in
- 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
- 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
- esac
- ;;
- stop)
- [ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
- do_stop
- case "$?" in
- 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
- 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
- esac
- ;;
- status)
- status_of_proc "$DAEMON" "$NAME" && exit 0 || exit $?
- ;;
- #reload|force-reload)
- #
- # If do_reload() is not implemented then leave this commented out
- # and leave 'force-reload' as an alias for 'restart'.
- #
- #log_daemon_msg "Reloading $DESC" "$NAME"
- #do_reload
- #log_end_msg $?
- #;;
- restart|force-reload)
- #
- # If the "reload" option is implemented then remove the
- # 'force-reload' alias
- #
- log_daemon_msg "Restarting $DESC" "$NAME"
- do_stop
- case "$?" in
- 0|1)
- do_start
- case "$?" in
- 0) log_end_msg 0 ;;
- 1) log_end_msg 1 ;; # Old process is still running
- *) log_end_msg 1 ;; # Failed to start
- esac
- ;;
- *)
- # Failed to stop
- log_end_msg 1
- ;;
- esac
- ;;
- *)
- #echo "Usage: $SCRIPTNAME {start|stop|restart|reload|force-reload}" >&2
- echo "Usage: $SCRIPTNAME {start|stop|status|restart|force-reload}" >&2
- exit 3
- ;;
-esac
-
-:
diff --git a/debian/manpage.1.ex b/debian/manpage.1.ex
deleted file mode 100644
index 5c497b9..0000000
--- a/debian/manpage.1.ex
+++ /dev/null
@@ -1,56 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" (C) Copyright 2015 Olivier Sallou <osallou at debian.org>,
-.\"
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH PYTHON-CUTADAPT SECTION "August 17, 2015"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-python-cutadapt \- program to do something
-.SH SYNOPSIS
-.B python-cutadapt
-.RI [ options ] " files" ...
-.br
-.B bar
-.RI [ options ] " files" ...
-.SH DESCRIPTION
-This manual page documents briefly the
-.B python-cutadapt
-and
-.B bar
-commands.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBpython-cutadapt\fP is a program that...
-.SH OPTIONS
-These programs follow the usual GNU command line syntax, with long
-options starting with two dashes (`-').
-A summary of options is included below.
-For a complete description, see the Info files.
-.TP
-.B \-h, \-\-help
-Show summary of options.
-.TP
-.B \-v, \-\-version
-Show version of program.
-.SH SEE ALSO
-.BR bar (1),
-.BR baz (1).
-.br
-The programs are documented fully by
-.IR "The Rise and Fall of a Fooish Bar" ,
-available via the Info system.
diff --git a/debian/manpage.sgml.ex b/debian/manpage.sgml.ex
deleted file mode 100644
index f4f89d9..0000000
--- a/debian/manpage.sgml.ex
+++ /dev/null
@@ -1,154 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
- <!ENTITY dhsurname "<surname>SURNAME</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>August 17, 2015</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
- <!ENTITY dhemail "<email>osallou at debian.org</email>">
- <!ENTITY dhusername "Olivier Sallou">
- <!ENTITY dhucpackage "<refentrytitle>PYTHON-CUTADAPT</refentrytitle>">
- <!ENTITY dhpackage "python-cutadapt">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>program to do something</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
-
- <arg><option>-e <replaceable>this</replaceable></option></arg>
-
- <arg><option>--example <replaceable>that</replaceable></option></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> and <command>bar</command>
- commands.</para>
-
- <para>This manual page was written for the &debian; distribution
- because the original program does not have a manual page.
- Instead, it has documentation in the &gnu;
- <application>Info</application> format; see below.</para>
-
- <para><command>&dhpackage;</command> is a program that...</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
-
- <para>These programs follow the usual &gnu; command line syntax,
- with long options starting with two dashes (`-'). A summary of
- options is included below. For a complete description, see the
- <application>Info</application> files.</para>
-
- <variablelist>
- <varlistentry>
- <term><option>-h</option>
- <option>--help</option>
- </term>
- <listitem>
- <para>Show summary of options.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-v</option>
- <option>--version</option>
- </term>
- <listitem>
- <para>Show version of program.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
-
- <para>bar (1), baz (1).</para>
-
- <para>The programs are documented fully by <citetitle>The Rise and
- Fall of a Fooish Bar</citetitle> available via the
- <application>Info</application> system.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (and may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the terms of the &gnu; General Public License, Version 2 any
- later version published by the Free Software Foundation.
- </para>
- <para>
- On Debian systems, the complete text of the GNU General Public
- License can be found in /usr/share/common-licenses/GPL.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
-sgml-indent-step:2
-sgml-indent-data:t
-sgml-parent-document:nil
-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
diff --git a/debian/manpage.xml.ex b/debian/manpage.xml.ex
deleted file mode 100644
index b9684e1..0000000
--- a/debian/manpage.xml.ex
+++ /dev/null
@@ -1,291 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
-"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
-
-<!--
-
-`xsltproc -''-nonet \
- -''-param man.charmap.use.subset "0" \
- -''-param make.year.ranges "1" \
- -''-param make.single.year.ranges "1" \
- /usr/share/xml/docbook/stylesheet/docbook-xsl/manpages/docbook.xsl \
- manpage.xml'
-
-A manual page <package>.<section> will be generated. You may view the
-manual page with: nroff -man <package>.<section> | less'. A typical entry
-in a Makefile or Makefile.am is:
-
-DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl/manpages/docbook.xsl
-XP = xsltproc -''-nonet -''-param man.charmap.use.subset "0"
-
-manpage.1: manpage.xml
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The XSL files are in
-docbook-xsl. A description of the parameters you can use can be found in the
-docbook-xsl-doc-* packages. Please remember that if you create the nroff
-version in one of the debian/rules file targets (such as build), you will need
-to include xsltproc and docbook-xsl in your Build-Depends control field.
-Alternatively use the xmlto command/package. That will also automatically
-pull in xsltproc and docbook-xsl.
-
-Notes for using docbook2x: docbook2x-man does not automatically create the
-AUTHOR(S) and COPYRIGHT sections. In this case, please add them manually as
-<refsect1> ... </refsect1>.
-
-To disable the automatic creation of the AUTHOR(S) and COPYRIGHT sections
-read /usr/share/doc/docbook-xsl/doc/manpages/authors.html. This file can be
-found in the docbook-xsl-doc-html package.
-
-Validation can be done using: `xmllint -''-noout -''-valid manpage.xml`
-
-General documentation about man-pages and man-page-formatting:
-man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
-
--->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "FIRSTNAME">
- <!ENTITY dhsurname "SURNAME">
- <!-- dhusername could also be set to "&dhfirstname; &dhsurname;". -->
- <!ENTITY dhusername "Olivier Sallou">
- <!ENTITY dhemail "osallou at debian.org">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1) and
- http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
- <!ENTITY dhsection "SECTION">
- <!-- TITLE should be something like "User commands" or similar (see
- http://www.tldp.org/HOWTO/Man-Page/q2.html). -->
- <!ENTITY dhtitle "python-cutadapt User Manual">
- <!ENTITY dhucpackage "PYTHON-CUTADAPT">
- <!ENTITY dhpackage "python-cutadapt">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <authorgroup>
- <author>
- <firstname>&dhfirstname;</firstname>
- <surname>&dhsurname;</surname>
- <contrib>Wrote this manpage for the Debian system.</contrib>
- <address>
- <email>&dhemail;</email>
- </address>
- </author>
- </authorgroup>
- <copyright>
- <year>2007</year>
- <holder>&dhusername;</holder>
- </copyright>
- <legalnotice>
- <para>This manual page was written for the Debian system
- (and may be used by others).</para>
- <para>Permission is granted to copy, distribute and/or modify this
- document under the terms of the GNU General Public License,
- Version 2 or (at your option) any later version published by
- the Free Software Foundation.</para>
- <para>On Debian systems, the complete text of the GNU General Public
- License can be found in
- <filename>/usr/share/common-licenses/GPL</filename>.</para>
- </legalnotice>
- </refentryinfo>
- <refmeta>
- <refentrytitle>&dhucpackage;</refentrytitle>
- <manvolnum>&dhsection;</manvolnum>
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>program to do something</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <!-- These are several examples, how syntaxes could look -->
- <arg choice="plain"><option>-e <replaceable>this</replaceable></option></arg>
- <arg choice="opt"><option>--example=<parameter>that</parameter></option></arg>
- <arg choice="opt">
- <group choice="req">
- <arg choice="plain"><option>-e</option></arg>
- <arg choice="plain"><option>--example</option></arg>
- </group>
- <replaceable class="option">this</replaceable>
- </arg>
- <arg choice="opt">
- <group choice="req">
- <arg choice="plain"><option>-e</option></arg>
- <arg choice="plain"><option>--example</option></arg>
- </group>
- <group choice="req">
- <arg choice="plain"><replaceable>this</replaceable></arg>
- <arg choice="plain"><replaceable>that</replaceable></arg>
- </group>
- </arg>
- </cmdsynopsis>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <!-- Normally the help and version options make the programs stop
- right after outputting the requested information. -->
- <group choice="opt">
- <arg choice="plain">
- <group choice="req">
- <arg choice="plain"><option>-h</option></arg>
- <arg choice="plain"><option>--help</option></arg>
- </group>
- </arg>
- <arg choice="plain">
- <group choice="req">
- <arg choice="plain"><option>-v</option></arg>
- <arg choice="plain"><option>--version</option></arg>
- </group>
- </arg>
- </group>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1 id="description">
- <title>DESCRIPTION</title>
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> and <command>bar</command>
- commands.</para>
- <para>This manual page was written for the Debian distribution
- because the original program does not have a manual page.
- Instead, it has documentation in the GNU <citerefentry>
- <refentrytitle>info</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry> format; see below.</para>
- <para><command>&dhpackage;</command> is a program that...</para>
- </refsect1>
- <refsect1 id="options">
- <title>OPTIONS</title>
- <para>The program follows the usual GNU command line syntax,
- with long options starting with two dashes (`-'). A summary of
- options is included below. For a complete description, see the
- <citerefentry>
- <refentrytitle>info</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry> files.</para>
- <variablelist>
- <!-- Use the variablelist.term.separator and the
- variablelist.term.break.after parameters to
- control the term elements. -->
- <varlistentry>
- <term><option>-e <replaceable>this</replaceable></option></term>
- <term><option>--example=<replaceable>that</replaceable></option></term>
- <listitem>
- <para>Does this and that.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-h</option></term>
- <term><option>--help</option></term>
- <listitem>
- <para>Show summary of options.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-v</option></term>
- <term><option>--version</option></term>
- <listitem>
- <para>Show version of program.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1 id="files">
- <title>FILES</title>
- <variablelist>
- <varlistentry>
- <term><filename>/etc/foo.conf</filename></term>
- <listitem>
- <para>The system-wide configuration file to control the
- behaviour of <application>&dhpackage;</application>. See
- <citerefentry>
- <refentrytitle>foo.conf</refentrytitle>
- <manvolnum>5</manvolnum>
- </citerefentry> for further details.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><filename>${HOME}/.foo.conf</filename></term>
- <listitem>
- <para>The per-user configuration file to control the
- behaviour of <application>&dhpackage;</application>. See
- <citerefentry>
- <refentrytitle>foo.conf</refentrytitle>
- <manvolnum>5</manvolnum>
- </citerefentry> for further details.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1 id="environment">
- <title>ENVIRONMENT</title>
- <variablelist>
- <varlistentry>
- <term><envar>FOO_CONF</envar></term>
- <listitem>
- <para>If used, the defined file is used as configuration
- file (see also <xref linkend="files"/>).</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1 id="diagnostics">
- <title>DIAGNOSTICS</title>
- <para>The following diagnostics may be issued
- on <filename class="devicefile">stderr</filename>:</para>
- <variablelist>
- <varlistentry>
- <term><errortext>Bad configuration file. Exiting.</errortext></term>
- <listitem>
- <para>The configuration file seems to contain a broken configuration
- line. Use the <option>--verbose</option> option, to get more info.
- </para>
- </listitem>
- </varlistentry>
- </variablelist>
- <para><command>&dhpackage;</command> provides some return codes, that can
- be used in scripts:</para>
- <segmentedlist>
- <segtitle>Code</segtitle>
- <segtitle>Diagnostic</segtitle>
- <seglistitem>
- <seg><errorcode>0</errorcode></seg>
- <seg>Program exited successfully.</seg>
- </seglistitem>
- <seglistitem>
- <seg><errorcode>1</errorcode></seg>
- <seg>The configuration file seems to be broken.</seg>
- </seglistitem>
- </segmentedlist>
- </refsect1>
- <refsect1 id="bugs">
- <!-- Or use this section to tell about upstream BTS. -->
- <title>BUGS</title>
- <para>The program is currently limited to only work
- with the <package>foobar</package> library.</para>
- <para>The upstreams <acronym>BTS</acronym> can be found
- at <ulink url="http://bugzilla.foo.tld"/>.</para>
- </refsect1>
- <refsect1 id="see_also">
- <title>SEE ALSO</title>
- <!-- In alpabetical order. -->
- <para><citerefentry>
- <refentrytitle>bar</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>, <citerefentry>
- <refentrytitle>baz</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>, <citerefentry>
- <refentrytitle>foo.conf</refentrytitle>
- <manvolnum>5</manvolnum>
- </citerefentry></para>
- <para>The programs are documented fully by <citetitle>The Rise and
- Fall of a Fooish Bar</citetitle> available via the <citerefentry>
- <refentrytitle>info</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry> system.</para>
- </refsect1>
-</refentry>
-
diff --git a/debian/menu.ex b/debian/menu.ex
deleted file mode 100644
index 0e36bf2..0000000
--- a/debian/menu.ex
+++ /dev/null
@@ -1,2 +0,0 @@
-?package(python-cutadapt):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
- title="python-cutadapt" command="/usr/bin/python-cutadapt"
diff --git a/debian/postinst.ex b/debian/postinst.ex
deleted file mode 100644
index 6150205..0000000
--- a/debian/postinst.ex
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/sh
-# postinst script for python-cutadapt
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see https://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- configure)
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/postrm.ex b/debian/postrm.ex
deleted file mode 100644
index 6590d2c..0000000
--- a/debian/postrm.ex
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/sh
-# postrm script for python-cutadapt
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postrm> `remove'
-# * <postrm> `purge'
-# * <old-postrm> `upgrade' <new-version>
-# * <new-postrm> `failed-upgrade' <old-version>
-# * <new-postrm> `abort-install'
-# * <new-postrm> `abort-install' <old-version>
-# * <new-postrm> `abort-upgrade' <old-version>
-# * <disappearer's-postrm> `disappear' <overwriter>
-# <overwriter-version>
-# for details, see https://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- ;;
-
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/preinst.ex b/debian/preinst.ex
deleted file mode 100644
index 63c8d59..0000000
--- a/debian/preinst.ex
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/sh
-# preinst script for python-cutadapt
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <new-preinst> `install'
-# * <new-preinst> `install' <old-version>
-# * <new-preinst> `upgrade' <old-version>
-# * <old-preinst> `abort-upgrade' <new-version>
-# for details, see https://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- install|upgrade)
- ;;
-
- abort-upgrade)
- ;;
-
- *)
- echo "preinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/prerm.ex b/debian/prerm.ex
deleted file mode 100644
index e7ff915..0000000
--- a/debian/prerm.ex
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# prerm script for python-cutadapt
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <prerm> `remove'
-# * <old-prerm> `upgrade' <new-version>
-# * <new-prerm> `failed-upgrade' <old-version>
-# * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
-# * <deconfigured's-prerm> `deconfigure' `in-favour'
-# <package-being-installed> <version> `removing'
-# <conflicting-package> <version>
-# for details, see https://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- remove|upgrade|deconfigure)
- ;;
-
- failed-upgrade)
- ;;
-
- *)
- echo "prerm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/python-cutadapt.cron.d.ex b/debian/python-cutadapt.cron.d.ex
deleted file mode 100644
index 6a6faba..0000000
--- a/debian/python-cutadapt.cron.d.ex
+++ /dev/null
@@ -1,4 +0,0 @@
-#
-# Regular cron jobs for the python-cutadapt package
-#
-0 4 * * * root [ -x /usr/bin/python-cutadapt_maintenance ] && /usr/bin/python-cutadapt_maintenance
diff --git a/debian/python-cutadapt.default.ex b/debian/python-cutadapt.default.ex
deleted file mode 100644
index 94c93ba..0000000
--- a/debian/python-cutadapt.default.ex
+++ /dev/null
@@ -1,10 +0,0 @@
-# Defaults for python-cutadapt initscript
-# sourced by /etc/init.d/python-cutadapt
-# installed at /etc/default/python-cutadapt by the maintainer scripts
-
-#
-# This is a POSIX shell fragment
-#
-
-# Additional options that are passed to the Daemon.
-DAEMON_OPTS=""
diff --git a/debian/python-cutadapt.doc-base.EX b/debian/python-cutadapt.doc-base.EX
deleted file mode 100644
index 0669eb7..0000000
--- a/debian/python-cutadapt.doc-base.EX
+++ /dev/null
@@ -1,20 +0,0 @@
-Document: python-cutadapt
-Title: Debian python-cutadapt Manual
-Author: <insert document author here>
-Abstract: This manual describes what python-cutadapt is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/python-cutadapt/python-cutadapt.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/python-cutadapt/python-cutadapt.ps.gz
-
-Format: text
-Files: /usr/share/doc/python-cutadapt/python-cutadapt.text.gz
-
-Format: HTML
-Index: /usr/share/doc/python-cutadapt/html/index.html
-Files: /usr/share/doc/python-cutadapt/html/*.html
diff --git a/debian/python-cutadapt.manpages b/debian/python-cutadapt.manpages
new file mode 100644
index 0000000..dcf4553
--- /dev/null
+++ b/debian/python-cutadapt.manpages
@@ -0,0 +1 @@
+debian/cutadapt.man1
diff --git a/debian/python3-cutadapt.manpages b/debian/python3-cutadapt.manpages
new file mode 100644
index 0000000..2e88559
--- /dev/null
+++ b/debian/python3-cutadapt.manpages
@@ -0,0 +1 @@
+debian/cutadapt3.man1
diff --git a/debian/rules b/debian/rules
index 5c1cebc..caa7d6e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,16 +16,16 @@ include /usr/share/dpkg/default.mk
# package maintainers to append LDFLAGS
#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+export PYBUILD_NAME=cutadapt
+
# main packaging script based on dh7 syntax
%:
- dh $@
+ dh $@ --with python2,python3 --buildsystem=pybuild
-# dh_make generated override targets
-# This is example for Cmake (See https://bugs.debian.org/641051 )
-#override_dh_auto_configure:
-# dh_auto_configure -- \
-# -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+override_dh_install:
+ dh_install
+ mv debian/python3-cutadapt/usr/bin/cutadapt debian/python3-cutadapt/usr/bin/cutadapt3
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..48e75cd
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=uversionmangle=s/(rc|a|b|c)/~$1/ \
+http://pypi.debian.net/cutadapt/cutadapt-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
\ No newline at end of file
diff --git a/debian/watch.ex b/debian/watch.ex
deleted file mode 100644
index d14e38d..0000000
--- a/debian/watch.ex
+++ /dev/null
@@ -1,23 +0,0 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 3 file
-version=3
-
-# Uncomment to examine a Webpage
-# <Webpage URL> <string match>
-#http://www.example.com/downloads.php python-cutadapt-(.*)\.tar\.gz
-
-# Uncomment to examine a Webserver directory
-#http://www.example.com/pub/python-cutadapt-(.*)\.tar\.gz
-
-# Uncommment to examine a FTP server
-#ftp://ftp.example.com/pub/python-cutadapt-(.*)\.tar\.gz debian uupdate
-
-# Uncomment to find new files on sourceforge, for devscripts >= 2.9
-# http://sf.net/python-cutadapt/python-cutadapt-(.*)\.tar\.gz
-
-# Uncomment to find new files on GooglePages
-# http://example.googlepages.com/foo.html python-cutadapt-(.*)\.tar\.gz
--
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